Biosynthesis of -p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics

Background: The non-proteinogenic amino acid p-hydroxyphenylglycine is a crucial component of certain peptidic natural products synthesized by a non-ribosomal peptide synthetase mechanism. In particular, for the vancomycin group of antibiotics p-hydroxyphenylglycine plays a structural role in formation of the rigid conformation of the central heptapeptide aglycone in addition to being the site of glycosylation. Initial labeling studies suggested tyrosine was a precursor of p-hydroxyphenylglycine but the specific steps in p-hydroxyphenylglycine biosynthesis remained unknown. Recently, the sequencing of the chloroeremomycin gene cluster from Amycolatopsis orientalis gave new insights into the biosynthetic pathway and allowed for the prediction of a four enzyme pathway leading to -p-hydroxyphenylglycine from the common metabolite prephenate.Results: We have characterized three of the four proposed enzymes of the -p-hydroxyphenylglycine biosynthetic pathway. The three enzymes are encoded by open reading frames (ORFs) 21, 22 and 17 (ORF21: [PCZA361.1, O52791, CAA11761]; ORF22: [PCZA361.2, O52792, CAA11762]; ORF17: [PCZA361.25, O52815, CAA11790]), of the chloroeremomycin biosynthetic gene cluster and we show they have p-hydroxymandelate synthase, p-hydroxymandelate oxidase and -p-hydroxyphenylglycine transaminase activities, respectively.Conclusions: The -p-hydroxyphenylglycine biosynthetic pathway shown here is proposed to be the paradigm for how this non-proteinogenic amino acid is synthesized by microorganisms incorporating it into peptidic natural products. This conclusion is supported by the finding of homologs for the four -p-hydroxyphenylpyruvate biosynthetic enzymes in four organisms known to synthesize peptidic natural products that contain p-hydroxyphenylglycine. Three of the enzymes are proposed to function in a cyclic manner in vivo with -tyrosine being both the amino donor for -p-hydroxyphenylglycine and a source of p-hydroxyphenylpyruvate, an intermediate in the biosynthetic pathway.     

Photoinduced multi-mode quantum dynamics of pyrrole at the – conical intersections

The photoinduced dynamics of pyrrole at the – S₀ and – S₀ conical intersections has been investigated by multi-mode time-dependent quantum wave-packet calculations. Diabatic potential-energy surfaces have been constructed for both conical intersection using accurate multi-reference ab initio electronic-structure calculations. In addition to the NH stretching coordinate, the three (four) symmetry-allowed coupling modes of A₂ (B₁) symmetry have been considered for the – S₀ (– S₀) conical intersections. Wave-packet dynamics calculations have been performed for three-dimensional models, taking account of the two dominant coupling modes of each conical intersection. The electronic population-transfer processes at the conical intersections, the branching ratio for the dissociation to the ground and excited states of the pyrrolyl radical, and their dependence on the initial preparation of the system have been investigated. It is shown that the excitation of the NH stretching mode strongly enhances the photodissociation rate, while the excitation of the strongest coupling mode has a pronounced effect on the branching ratio of the photodissociation process. Although the inclusion of the second (weaker) coupling mode has little effect on the electronic population dynamics, it leads to interesting changes of the nodal pattern of the wave packet at the conical intersections. The calculations provide insight into the effect of the multiple coupling modes on the process of direct photodissociation through a conical intersection.     

Fragmentation of the valence electronic states of NF3 studied by threshold photoelectron–photoion coincidence spectroscopy

The valence threshold photoelectron spectrum of NF₃ is reported for the first time in the literature, and threshold photoelectron–photoion coincidence (TPEPICO) spectroscopy has measured, state-selectively, the decay dynamics of the valence states of NF₃⁺ in the range 13–23 eV. Vacuum–UV radiation from the Daresbury synchrotron source dispersed by a 1 m Seya-Namioka monochromator photoionises the parent molecules. Electrons and ions are detected by threshold electron analysis and time-of-flight mass spectrometry, respectively. TPEPICO spectra are recorded continuously as a function of photon energy, allowing coincidence ion yields of the fragment ions and the breakdown diagram to be obtained. A comparison of the integrated threshold photoelectron and the total ion signals as a function of energy suggests that, in the range 16–19 eV, autoionisation via Rydberg states of NF₃ makes a significant contribution to the production of threshold electrons. The 50% crossover energy for production of NF₂⁺ from NF₃⁺ is determined to be 14.10±0.05 eV. The first onsets for NF₂⁺ and NF⁺ production are 13.95±0.05 and 17.6±0.1 eV, respectively. The majority of the Franck–Condon region of the ground state of NF₃⁺ is stable with respect to dissociation to NF₂⁺, whereas the unresolved states and most of the state dissociate exclusively to NF₂⁺. The and states dissociate to NF⁺. Translational kinetic energy releases have been measured in NF₂⁺ and NF⁺ at the energies of the Franck–Condon maxima of the valence states of NF₃⁺. The results are compared with models assuming statistical and impulsive dissociation. The Ã/ states of NF₃⁺ dissociate directly from the excited-state potential energy surface to NF₂⁺, whereas the higher-lying state probably dissociates off the ground-state surface following rapid internal conversion. It is not possible to correlate unambiguously the formation of NF⁺ with either F₂ or 2F, although on energetic grounds the latter products are more likely. Assuming that the neutral products are 2F, no information is obtained whether the two N–F bonds break simultaneously or sequentially.     

Steady and dynamic rheological behaviors of sodium carboxymethyl cellulose entangled semi-dilute solution with opposite charged surfactant dodecyl-trimethylammonium bromide

The steady and dynamic rheological behaviors of sodium carboxymethyl cellulose (NaCMC) entangled semi-dilute solution filled with different concentrations of dodecyl-trimethylammonium bromide (C₁₂TAB) were investigated. The results reveal that the zero shear rate viscosity (η₀) and dynamic modules (G′and G″) increase with C₁₂TAB concentration (C_s), and there exist three scaling regions divided by two critical C₁₂TAB concentrations (C₁, C₂ and , respectively, from steady and dynamic tests). The increase of viscosity and modules with C_s is ascribed to formation of network due to C₁₂TAB micelles bridging NaCMC chains. The two critical C₁₂TAB concentrations implies that the structure evolution of NaCMC–C₁₂TAB complex is exposed to three states with increasing C_s, i.e., no network formation, network extent progressive formation and perfect network formation, respectively. Moreover, are a little lower than C₁, C₂, indicating that the dynamic test is more sensitive to detect the structure change of the complex as compared with steady test. Furthermore, it is found that as NaCMC concentration increases, , and increase.     

Intense laser-induced decomposition of mass-selected 2-, 3-, and 4-methylaniline cations

Photodecomposition processes of 2-, 3-, and 4-methylaniline cations induced by a moderately intense (10¹¹ W/cm²) visible nanosecond laser field and an intense (10¹⁵ W/cm²) UV femtosecond laser field have been investigated using a tandem mass spectrometer. Highly unsaturated fragment cations such as and are dominantly produced by the nanosecond laser, while less unsaturated smaller fragment cations such as , and are produced mainly by the femtosecond laser. Ab initio calculations have also been performed to estimate the stable geometrical structures of and and those of possible intermediate ring compounds for discussing the photodecomposition pathways in intense laser fields.     

Hexachloroiridate(IV) as a redox probe for the electrochemical discrimination of B-DNA and M-DNA monolayers on gold

This paper demonstrates the effectiveness of using the redox couple to investigate DNA monolayers, and compares the potential advantages of this system to the standard redox couple. B-DNA monolayers were converted to M-DNA by incubation in buffer containing 0.4 mM Zn²⁺ at pH 8.6 and studied by cyclic voltammetry (CV), impedance spectroscopy (IS) and chronoamperometry (CA) with . Compared to B-DNA, M-DNA showed significant changes in CV, IS and CA spectra. However, only small changes were observed when the monolayers were incubated in Mg²⁺ at pH 8.6 or in Zn²⁺ at pH 6.0. The heterorgeneous electron-transfer rate (k_ET) between the redox probe and the surface of a bare gold electrode was determined to be 5.7 × 10⁻³ cm/s. For a B-DNA modified electrode, the k_ET through the monolayer was too slow to be measured. However, under M-DNA conditions, a k_ET of 1.5 × 10⁻³ cm/s was reached. As well, the percent change in resistance to charge transfer, measured by IS, was used to illustrate the dependence of M-DNA formation on pH. This result is consistent with Zn²⁺ ions replacing the imino protons on thymine and guanine residues. The redox couple was also effective in differentiating between single-stranded and double-stranded DNA during de-hybridization and rehybridization experiments.     

First principles study of the structure, electronic state and stability of cations

Structural and electronic properties of semiconductor binary microclusters cations have been investigated using the B3LYP-DFT method in the ranges of n=1, 2 and m=1–7. Full structural optimization, adiabatic ionization potentials calculation and frequency analysis are performed with the basis of 6-311+G(d). The charged-induced structural changes in these cations have been discussed. The strong As–As bond is also favored over Al–As bonds in the cations in comparison with corresponding neutral cluster. With As_m forming the base, adding Al atom(s) in different positions would find the stable structures of cations quickly and correctly. , , and are predicted to be species with high stabilities and possible to be produced experimentally.     

Electron transfer properties and electrocatalytic behavior of tyrosinase on ZnO nanorod

In this work, the adsorption of tyrosinase on ZnO nanorods and its electrocatalytic behaviors were investigated. The mushroom tyrosinase with low isoelectric point was expected to adhere on the positively charged surface of ZnO nanorods by electrostatic attraction in a neutral solution. Scanning electron microscope images and spectroscopic analysis demonstrated the adsorption of tyrosinase on ZnO nanorods and the adsorbed tyrosinase remain its bioactivity to a large extent. In the presence of tyrosinase, a roughly and cyathiform of nanosized ZnO films was obtained. This open, three-dimensioned ramiform structure made the move through and exchange the electron with GCE more easily, and thus accelerating the electron transfer between electroactive and GCE. The adsorbed tyrosinase could catalyze the oxidation of phenol and catechol. The linear concentration ranges were from 0.02 to 0.1 mM and 0.01 to 0.4 mM, for phenol and catechol, respectively. The apparent Michaelis-menten constant , a reflection of the enzymatic affinity, was 0.24 mM for phenol and 1.75 mM for catechol, which suggests a large affinity to phenolic compound. The proposed methods presented a way for further studies of the immobilization and electrochemistry of proteins on nanostructured materials.     

Vibrational relaxation on the mixed vibronic levels of the and states in all-trans-neurosporene as revealed by subpicosecond time-resolved, stimulated emission and transient absorption spectroscopy

In all-trans-neurosporene, whose level is lower than the level by one vibrational quantum, the following two steps of vibrational relaxation from the mixed vibronic states were identified, in the order, stimulated emission stimulated emission transient absorption. The stimulated emission patterns were simulated by the use of Franck–Condon factors in the transitions from the pair of mixed vibronic levels down to the ground vibronic levels. The vibronic levels of the mixed and state were characterized theoretically based on the diabatic approximation.     

Surface properties and aggregate morphology of partially fluorinated carboxylate-type anionic gemini surfactants

Three anionic homologues of a novel partially fluorinated carboxylate-type anionic gemini surfactant, N,N′-di(3-perfluoroalkyl-2-hydroxypropyl)-N,N′-diacetic acid ethylenediamine (2 edda, where n represents the number of carbon atoms in the fluorocarbon chain (4, 6, and 8)) were synthesized. In these present gemini surfactants, the relatively small carboxylic acid moieties form hydrophilic head groups. The surface properties or structures of the aggregates of these surfactants are strongly influenced by the nonflexible fluorocarbons and small head groups; this is because these surfactants have a closely packed molecular structure. The equilibrium surface tension properties of these surfactants were measured at 298.2 K for various fluorocarbon chain lengths. The plot of the logarithm of the critical micelle concentration (cmc) against the fluorocarbon chain lengths for 2 edda (n = 4, 6, and 8) showed a minimum for n = 6. Furthermore, the lowest surface tension of 2 edda at the cmc was 16.4 mN m⁻¹. Such unique behavior has not been observed even in the other fluorinated surfactants. Changes in the shapes and sizes of these surfactant aggregate with concentration were investigated by dynamic light scattering and transmission electron microscopy (TEM). The TEM micrographs showed that in an aqueous alkali solution, 2 edda mainly formed aggregates with stringlike (n = 4), cagelike (n = 6), and distorted bilayer structures (n = 8). The morphological changes in the aggregates were affected by the molecular structure composed of nonflexible fluorocarbon chains and flexible hydrocarbon chains.     

The diverse behaviour of the P–Cl bonds in the spiro–cis–ansa spermidine derivative cyclotriphosphazene towards mono-functional nucleophilic reagents

A number of new spiro–ansa spermidine derivative cyclotriphosphazenes (2–10) is synthesized in order to provide insight into the reaction mechanism for nucleophilic substitution. The structures of the compounds were determined by elemental analysis, mass (MS), ¹H, ¹⁹F (for 9) and ³¹P NMR spectroscopies. Compounds (2–8) and 9, 10 can be formed by a proton abstraction–chloride elimination and both the and reaction mechanisms, respectively.     

Is Cd2 truly a van der Waals molecule? Analysis of rotational profiles recorded at the , transitions

Rotational profiles of the ²²⁸Cd₂ isotopomer recorded in the (υ′, υ″) = (26, 0), (27, 0), (42, 0), (45, 0), (46, 0), (48, 0) vibrational bands of the transition were analysed. As a result, the , , , , and excited- as well as the ground-state rotational constants of the (¹¹⁴Cd)₂ were determined. The analysis allowed determining the absolute values for the and excited- and ground-state bond lengths, respectively. The obtained result – the – distinctly shorter than that obtained with assumption of pure ground-state van der Waals bonding, supports a theoretical prediction of a covalent admixture to the bonding. Analysis of the partially-resolved rotational profile recorded in the (υ′, υ″) = (38, 0) band of the same isotopomer recorded at the transition allowed estimating the rotational constant in the B1_u state.     

Franck–Condon simulation of photoelectron spectroscopy of HOO: Including Duschinsky effects

Geometry optimization and harmonic vibrational frequency calculations were performed on the and states of HOO and state of HOO⁻. The electron affinity and the term energy () of HOO were calculated at various theory levels. Franck–Condon analyses and spectral simulations were carried out on the and photodetachment processes. The spectral simulations of vibrational structures based on the computed Franck–Condon factors are in excellent agreement with the observed spectra. In addition, the equilibrium geometrical parameters of the state of HOO⁻ and state of HOO were obtained in the spectral simulations.     

Unique charge ordering of manganese in a new mixed valent phosphate

A new mixed-valent manganese phosphate, , has been synthesized using hydrothermal method. Its monoclinic C2/c structure (a=12.5506(16) Å, b=10.4816(18) Å, c=13.6723(10) Å, β=103.758(11)°) forms a 3D framework of MnO₆ octahedra, MnO₅ trigonal bipyramids, PO₄ and PO₃OH tetrahedra. The main structural feature of this phosphate deals with its [Mn₄O₁₆]_∞ chains running along , which are interconnected through PO₄ and PO₃OH tetrahedra, forming intersecting tunnels running along [110], and [001]. The geometry of the [Mn₄O₁₆]_∞ chains and the charge ordering of manganese in the latter are unique: they consist of trimeric units of divalent manganese “” alternating with single trivalent Mn^IIIO₆ octahedra along . In each “” unit one central Mn^IIO₆ octahedron shares two opposite edges with two Mn^IIO₅ trigonal bipyramids. Along , one Mn(II) octahedron alternates with one Mn(III) octahedron by sharing one corner. The relationships between the structure of this unique charge ordered phosphate and other manganese phosphates are discussed.     

Structures and properties of the tin-doped carbon clusters

A systemic density functional theory study of the tin-doped carbon clusters has been carried out using B3LYP method with TZP+ basis set. For each species, the electronic states, relative energies and geometries of various isomers are reported. Except for smaller SnC₂ and the largest , the Sn-terminated linear or quasi-linear isomer is the most stable structure for clusters. The electronic ground state is alternate between ³Σ (for n-odd member) and ¹Σ (for the n-even member) for linear SnC_n and invariably ²Π for linear and , except for SnC/SnC⁺/SnC⁻,, and . The incremental binding energy diagrams show that strong even–odd alternations in the cluster stability exist for both neutral SnC_n and anionic , with their n-even members being much more stable than the corresponding odd n − 1 and n + 1 ones, while for cationic , the alternation effect is less pronounced. These parity effects also reflect in the ionization potential and electron affinity curves. By comparing with the fragmentation energies accompanying various channels, the most favorable dissociation channel for each kind of the clusters are given. All these results are very similar to those obtained previously for the clusters.     

Solution thermodynamics near the liquid–liquid critical point. II. Excess second-order derivatives

We present a comprehensive study of the behaviour of excess second-order derivatives of binary mixtures near the liquid–liquid critical point. Specifically, excess (isobaric and isochoric) molar heat capacities ( and ), excess (isothermal and isentropic) compressibilities ( and ), and excess isobaric thermal expansivities () have been determined over the whole composition (x) range at atmospheric pressure and in the homogeneous region within (293.15–323.15) K. Results are consistent with the predictions of the current theory of critical phenomena. Remarkably, anomalous and curves in the critical region are observed. Such anomalies, which are reported here for the first time, are of significant size for and very mild in the case of , thereby indicating that volumetric effects at near-liquid–liquid criticality are, as expected, very small.     

DFT study of electronic structure and geometry of anionic silver clusters (n = 11, 12, 17)

Based on both total energy calculations and comparison of experimental and calculated characteristics of photoelectron spectra (PHES), the structural assignment of clusters and has been made using DFT model with recently developed S2LYP functional. The calculated characteristics of PHES for the assigned structures are in excellent agreement with the experimental ones. The electronic structure, geometry and energetic characteristics of low-lying isomers have also been studied. The calculated geometrical parameters of and clusters as well as the geometries of earlier established clusters have been compared with the geometrical characteristics of anionic sodium clusters. The structures of anionic silver and sodium clusters have been found to be very similar. The difference has been observed only for . Based on similarity of the geometries of silver and sodium clusters as well as on the comparison of calculated and experimental characteristics of PHES, the geometry of cluster has been assigned.     

Free-energy change of inserting halothane into different depths of a hydrated DMPC bilayer

Using the method of energy representation, we have calculated the free-energy change of inserting a halothane molecule into different depths of a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer at pressures of to . Our results show that the free-energy change is more negative within the membrane than in bulk water. The halothane distribution is diffuse, and the preferred location is near the headgroup. The pressure effect is found to be minimal within the pressure range examined, which corresponds to previous biological experimental conditions.     

Effect of salts on the excited state of pyranine as determined by steady-state fluorescence

Pyranine is a pH-sensitive fluorescent probe useful in the pH range of 4.5–8, and it has been extensively employed to determine pH inside cells, membranes and membrane models. The fluorescent properties of pyranine are a consequence of the excited states ROH^* and RO^−*. The prototropic equilibrium of these excited species has a much lower than that of the ground state. In this paper we determined the (1.42 ± 0.06) and the relative quantum yield of pyranine in the pH range of 1–8 by analyzing the component peaks of the steady-state of the dye's emission spectrum. As pyranine is very sensitive to the medium we studied the influence of salts formed by mono-, di-, and trivalent ions on the apparent . In all cases, the presence of salts reduced the apparent to varying degrees depending on the valence of the cations. The strategy used to obtain this information was a dual emission ratiometric method at 441 and 511 nm after excitation at 350 nm. The results obtained demonstrate that pyranine is suitable to determine the pH of aqueous solutions in the range of 1–3.5.